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- PDB-5ayg: Crystal Structure of the Human ROR gamma Ligand Binding Domain With 3g -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ayg | ||||||
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Title | Crystal Structure of the Human ROR gamma Ligand Binding Domain With 3g | ||||||
![]() | Nuclear receptor ROR-gamma | ||||||
![]() | DNA BINDING PROTEIN/INHIBITOR / Inhibitor / Complex / Nuclear Receptor / DNA BINDING PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() ligand-activated transcription factor activity / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...ligand-activated transcription factor activity / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Noguchi, M. / Doi, S. / Nomura, A. / Kikuwaka, M. / Murase, K. / Hirata, K. / Kamada, M. / Adachi, T. | ||||||
![]() | ![]() Title: SAR Exploration Guided by LE and Fsp(3): Discovery of a Selective and Orally Efficacious ROR gamma Inhibitor Authors: Hirata, K. / Kotoku, M. / Seki, N. / Maeba, T. / Maeda, K. / Hirashima, S. / Sakai, T. / Obika, S. / Hori, A. / Hase, Y. / Yamaguchi, T. / Katsuda, Y. / Hata, T. / Miyagawa, N. / Arita, K. / ...Authors: Hirata, K. / Kotoku, M. / Seki, N. / Maeba, T. / Maeda, K. / Hirashima, S. / Sakai, T. / Obika, S. / Hori, A. / Hase, Y. / Yamaguchi, T. / Katsuda, Y. / Hata, T. / Miyagawa, N. / Arita, K. / Nomura, Y. / Asahina, K. / Aratsu, Y. / Kamada, M. / Adachi, T. / Noguchi, M. / Doi, S. / Crowe, P. / Bradley, E. / Steensma, R. / Tao, H. / Fenn, M. / Babine, R. / Li, X. / Thacher, S. / Hashimoto, H. / Shiozaki, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.1 KB | Display | ![]() |
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PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bowS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29898.516 Da / Num. of mol.: 2 / Fragment: UNP residues 261-518 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.73 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Tris-HCl , pH 7.5, 0.5M Na/K tartrate, 2.5M, MPD PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 19, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→85.94 Å / Num. obs: 22021 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 6.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BOW Resolution: 2.6→85.94 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.347 / SU ML: 0.181 / Cross valid method: FREE R-VALUE / ESU R: 0.374 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.251 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→85.94 Å
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